Coupled Equilibrium Model of Hybridization Error for the DNA Microarray and Tag–Antitag Systems

@article{Rose07, abstract = {In this work, a detailed coupled equilibrium model is presented for predicting the ensemble average probability of hybridization error per chip-hybridized input strand, providing the first ensemble average method for estimating postannealing microarray/TAT system error rates. Following a detailed presentation of the model and implementation via the software package NucleicPark, under a mismatched statistical zipper model of duplex formation, error response is simulated for both mean-energy and randomly encoded TAT systems versus temperature and input concentration. Limiting expressions and simulated model behavior indicate the occurrence of a transition in hybridization error response, from a logarithmically convex function of temperature for excess inputs (high-error behavior), to a monotonic, log-linear function of temperature for dilute inputs (low-error behavior), a novel result unpredicted by uncoupled equilibrium models. Model scaling behavior for random encodings is investigated versus system size and strand-length. Application of the model to TAT system design is also undertaken, via the in silico evolution of a high-fidelity 100-strand TAT system, with an error response improved by nine standard deviations over the performance of the mean random encoding}, author = {Rose, John A. and Deaton, Russell J. and Hagiya, Masami and Suyama, Akira }, booktitle = {NanoBioscience, IEEE Transactions on}, citeulike-article-id = {2702881}, doi = {10.1109/TNB.2007.891896}, journal = {NanoBioscience, IEEE Transactions on}, keywords = {codeword\_design, microarrays, thermodynamics, universal\_microarrays}, number = {1}, pages = {18--27}, posted-at = {2008-04-22 20:38:30}, priority = {2}, title = {Coupled Equilibrium Model of Hybridization Error for the DNA Microarray and Tag\–Antitag Systems}, url = {http://dx.doi.org/10.1109/TNB.2007.891896}, volume = {6}, year = {2007} }

TY - JOUR ID - Rose07 L3 - citeulike-article-id:2702881 TI - Coupled Equilibrium Model of Hybridization Error for the DNA Microarray and Tag–Antitag Systems T2 - NanoBioscience, IEEE Transactions on JF - NanoBioscience, IEEE Transactions on VL - 6 IS - 1 SP - 18 EP - 27 N2 - In this work, a detailed coupled equilibrium model is presented for predicting the ensemble average probability of hybridization error per chip-hybridized input strand, providing the first ensemble average method for estimating postannealing microarray/TAT system error rates. Following a detailed presentation of the model and implementation via the software package NucleicPark, under a mismatched statistical zipper model of duplex formation, error response is simulated for both mean-energy and randomly encoded TAT systems versus temperature and input concentration. Limiting expressions and simulated model behavior indicate the occurrence of a transition in hybridization error response, from a logarithmically convex function of temperature for excess inputs (high-error behavior), to a monotonic, log-linear function of temperature for dilute inputs (low-error behavior), a novel result unpredicted by uncoupled equilibrium models. Model scaling behavior for random encodings is investigated versus system size and strand-length. Application of the model to TAT system design is also undertaken, via the in silico evolution of a high-fidelity 100-strand TAT system, with an error response improved by nine standard deviations over the performance of the mean random encoding KW - codeword_design KW - microarrays KW - thermodynamics KW - universal_microarrays AU - Rose, John AU - Deaton, Russell AU - Hagiya, Masami AU - Suyama, Akira PY - 2007/// UR - http://dx.doi.org/10.1109/TNB.2007.891896 ER -